From 9cb5137ef225888e5e466d2a339c5b78f07db5e0 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 26 Nov 2019 15:12:42 +0100 Subject: [PATCH 1/3] Better description --- README.md | 2 +- bin/cchecker.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f060b03..58a65d9 100644 --- a/README.md +++ b/README.md @@ -115,7 +115,7 @@ Currently documentation is available for the following systems: [Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account. Within the local clone of your fork add the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory. You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone. -Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. +Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to the alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. If you forget to do this, tests will fail and complain about that. Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information. diff --git a/bin/cchecker.py b/bin/cchecker.py index eb995fc..4290170 100644 --- a/bin/cchecker.py +++ b/bin/cchecker.py @@ -64,7 +64,7 @@ def check_config(Config, Github): sys.exit(0) else: #Maybe report what is missing here too - print("Tests don't seem to test these profiles properly!\n") + print("Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.\n") print(config_profiles.symmetric_difference(tests)) sys.exit(1) From da922b80059f7432737aa50f8140910bd9507f23 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 26 Nov 2019 15:45:33 +0100 Subject: [PATCH 2/3] Fix README --- README.md | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index ec810d7..2b18dcc 100644 --- a/README.md +++ b/README.md @@ -1,22 +1,21 @@ -# [![nf-core/configs](docs/images/nfcore-configs_logo.png)](https://github.com/nf-core/configs) +# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs) -[![Lint Status](https://github.com/nf-core/configs/workflows/nfcore%20configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/nfcore%20configs%20tests/badge.svg) +[![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg) A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions. ## Table of contents -* [![nf-core/configs](https://github.com/nf-core/configs)](#nf-coreconfigshttpsgithubcomnf-coreconfigs) - * [Table of contents](#table-of-contents) - * [Using an existing config](#using-an-existing-config) - * [Configuration and parameters](#configuration-and-parameters) - * [Offline usage](#offline-usage) - * [Adding a new config](#adding-a-new-config) - * [Checking user hostnames](#checking-user-hostnames) - * [Testing](#testing) - * [Documentation](#documentation) - * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) - * [Help](#help) +* [Table of contents](#table-of-contents) +* [Using an existing config](#using-an-existing-config) + * [Configuration and parameters](#configuration-and-parameters) + * [Offline usage](#offline-usage) +* [Adding a new config](#adding-a-new-config) +* [Checking user hostnames](#checking-user-hostnames) + * [Testing](#testing) + * [Documentation](#documentation) + * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) +* [Help](#help) ## Using an existing config From b756ce54a488e2f65a63830fb88c6289f98b3426 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 26 Nov 2019 16:09:08 +0100 Subject: [PATCH 3/3] Add genotoul fix --- conf/genotoul.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/genotoul.config b/conf/genotoul.config index 75ad2c4..8ad50b1 100644 --- a/conf/genotoul.config +++ b/conf/genotoul.config @@ -19,6 +19,7 @@ process { params { save_reference = true igenomes_ignore = true + igenomesIgnore = true //deprecated // Max resources requested by a normal node on genotoul. max_memory = 120.GB max_cpus = 48